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On 24/01/2012 9:24 PM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43BxWwK-NKGNZTBktg39b0w-xErnusO1CE=xmXBDG-wRA-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote">I have replaced all HW by H in
ffnonbonded.itp.After executing the command:<br>
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
<font size="3"><font face="Arial"><br>
</font></font><br>
I am getting this error:<font size="3"><font face="Arial"><br>
</font></font><br>
File input/output error:<font size="3"><font face="Arial"><br>
</font></font>dppc128.gro<font size="3"><font face="Arial"><br>
</font></font></div>
</blockquote>
<br>
This file likely does not exist. Use a file that exists.<br>
<br>
<blockquote
cite="mid:CAAx43BxWwK-NKGNZTBktg39b0w-xErnusO1CE=xmXBDG-wRA-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote"><font size="3"><font face="Arial">
<br>
</font></font>should I replace all HW with H (without
delecting numbers that is given in dppc128.pdb alongwith HW) in
dppc128.pdb file?<br>
</div>
</blockquote>
<br>
Think first. grompp hasn't complained about the contents of this
file, because it hasn't seen it. So don't make changes that aren't
in the tutorial that aren't fixing the problem.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAx43BxWwK-NKGNZTBktg39b0w-xErnusO1CE=xmXBDG-wRA-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote"><font face="Arial"><font size="3">
<pre>
</pre>
</font></font><br>
<br>
<br>
<br>
<br>
On Mon, Jan 23, 2012 at 6:41 PM, Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div><br>
<br>
Anushree Tripathi wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px
0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">I am
going through the Justin Lemku tutorial for KALP15 in
DPPC. I have<br>
reached step three, when I try to generate a trp file
for DPPC only by<br>
means of :<br>
<br>
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o
em.tpr<br>
<br>
I get the following warning:<br>
<br>
Fatal error:<br>
Atomtype OW not found<br>
<br>
Any idea as to what causes this problem?<br>
</blockquote>
<br>
</div>
</div>
You constructed the force field incorrectly by deleting or
commenting out a line (or more) related to OW. Re-check the
instructions provided in the tutorial.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu/"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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